Giving the wall thickness of hollow irregular pipe. Solidify not working well with the problem
I don't think the solidify modifier was meant to handle such complex geometry. If you apply the modifier, you can repair any irregularities by hand. 

The other idea would be to use the Shrinkwrap Modifier. It's ability to take the closest surface point as reference makes it pretty invulnerable to small holes.

Below is the result of a Cylinder with just 8 sides. I sandwiched the Shrinkwrap Modifier between two subsurfs. The first one decides how many verts the shrinker gets and the second is for smoothing. That way you can tweak how much inner surface structure leaks through.



All that's left is to apply the modifiers, join the meshes and stitch them together.